[English] 日本語
Yorodumi
- PDB-4dcz: Crystal structure of a domain from a mycoplasma genitalium termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dcz
TitleCrystal structure of a domain from a mycoplasma genitalium terminal organelle protein
ComponentsDnaJ-like protein MG200
KeywordsUNKNOWN FUNCTION / DIMER / INTRA-DOMAIN SYMMETRY AXIS
Function / homology
Function and homology information


chaperone cofactor-dependent protein refolding / unfolded protein binding / protein refolding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3600 / Enriched in aromatic and glycine residues box / EAGR domain superfamily / Enriched in aromatic and glycine Residues box / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain ...Alpha-Beta Plaits - #3600 / Enriched in aromatic and glycine residues box / EAGR domain superfamily / Enriched in aromatic and glycine Residues box / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DnaJ-like protein MG200
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsCalisto, B.M. / Martinelli, L. / Fita, I.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: The EAGR box structure: a motif involved in mycoplasma motility.
Authors: Calisto, B.M. / Broto, A. / Martinelli, L. / Querol, E. / Pinol, J. / Fita, I.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DnaJ-like protein MG200
B: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)21,8772
Polymers21,8772
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)10,9391
Polymers10,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DnaJ-like protein MG200


Theoretical massNumber of molelcules
Total (without water)10,9391
Polymers10,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.003, 81.003, 73.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsBIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC APPLY THE FOLLOWING TO CHAINS: A, B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 3 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

-
Components

#1: Protein DnaJ-like protein MG200


Mass: 10938.724 Da / Num. of mol.: 2 / Fragment: TO PROTEIN DOMAIN (UNP RESIDUES 124-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: G37 / Gene: MG200 / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47442

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 2000, 0.1 M SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-410.9790.979
SYNCHROTRONESRF ID14-420.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDJul 26, 2009MIRRORS
ADSC QUANTUM 315r2CCDNov 1, 2009MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSADMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 6450 / % possible obs: 74 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.066 / Net I/σ(I): 32.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.393 / % possible all: 90

-
Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→27.18 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 25.518 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.26 294 4.6 %RANDOM
Rwork0.203 ---
obs0.206 6418 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 0 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021954
X-RAY DIFFRACTIONr_bond_other_d0.0010.02640
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.891298
X-RAY DIFFRACTIONr_angle_other_deg0.93531536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46125.17258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30215142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.237154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7061.5540
X-RAY DIFFRACTIONr_mcbond_other0.1311.5226
X-RAY DIFFRACTIONr_mcangle_it1.3562860
X-RAY DIFFRACTIONr_scbond_it1.9023414
X-RAY DIFFRACTIONr_scangle_it3.0864.5438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 15 -
Rwork0.333 425 -
obs--96.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19752.16382.473128.299432.984538.52540.25750.0843-0.0031-0.1163-0.71980.1759-0.2917-1.23910.46230.77470.1163-0.04391.18460.19970.912214.826160.889349.6763
25.2715-2.7881-0.31958.4395-1.77937.5816-0.11730.20070.449-0.1744-0.023-0.2566-0.22710.2660.14020.087-0.03170.00310.0479-0.00140.06747.388854.406346.8424
36.4451-5.73255.784917.1509-3.62511.38830.15820.51050.2445-1.41740.022-0.2725-0.14220.6225-0.18020.1673-0.0520.08870.2975-0.01320.219913.809551.379140.8614
431.0296-28.406420.206531.0604-12.981519.23161.03620.4494-1.38630.5484-0.97991.95172.3396-0.459-0.05630.5464-0.28660.26390.3499-0.17440.44753.611930.282838.3254
55.953-0.6355-2.10064.88111.539710.3767-0.1085-0.0201-0.25390.11620.09360.14930.45970.20490.01490.04850.0228-0.0290.0171-0.00170.076910.591837.361738.8937
69.45271.1978-1.1182.48047.009828.450.13410.32370.66560.2085-0.00980.4189-0.5523-1.0312-0.12430.22340.16610.20450.1730.09270.35482.99243.415439.6848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 153
2X-RAY DIFFRACTION2A154 - 194
3X-RAY DIFFRACTION3A195 - 203
4X-RAY DIFFRACTION4B149 - 153
5X-RAY DIFFRACTION5B154 - 194
6X-RAY DIFFRACTION6B195 - 203

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more